Biologics, including protein-based drugs, are among the fastest growing categories of therapeutics under development today. While most biologics are made using mammalian cell systems, plant-based production systems provide a cost-effective approach to making new and similar medicines to fight disease. This process, called molecular pharming, uses a common plant pathogen, Agrobacterium tumefaciens, to deliver genes encoding for a specific protein product to the plant host, Nicotiana benthamiana. Although plant systems offer excellent potential for therapeutic protein production, barriers, such as plant host defense response, impact yield and limit wider adoption of the technology. In this thesis, I examine the molecular pharming pipeline from a systems-biology perspective to identify putative yield limiting factors. First, I explore the utilization of bioreactors as a substitute for shake flasks in bacterial biomass production. I examine variations in bacterial growth across the tested parameters and establish conditions necessary for consistent bacterial culturing. Through proteomic profiling of cultures under each growth condition, I identify distinct and growth-specific responses in bacterial protein abundance shedding light on the functional roles of these proteins that may influence bacterial processes involved in successful agroinfiltration and transformation. Next, I investigate the impact of time on bacterial culture preparation in agroinfiltration medium. I reveal distinct protein profiles associated with different bacterial treatment conditions and exposure timings, particularly in relation to pathogenesis, motility, and nutrient acquisition systems. These results indicate a progressive cellular remodeling of the bacterium over time to highlight the interconnectedness of pathogenesis and chemotaxis-related proteins with transport and metabolism. Finally, I investigate the infectome of N. benthamiana and A. tumefaciens to reveal distinctive patterns of bacterial protein production associated with each growth condition, which directly impact plant defense responses and the production of the target protein over time. By combining proteomic and metabolomics profiling, I detect the fluctuation of secondary metabolite production throughout the infection process, providing new insights into the intricate modulation of the dual biological systems. My findings suggest that bacterial growth in bioreactors may facilitate the evasion of early plant defense responses against A. tumefaciens. Overall, this thesis contributes to the knowledge of molecular pharming and identifies specific factors that may limit the yield of recombinant proteins.